sankaranlab · bschilder · Jan 3, 2023 · Jan 3, 2023 · Jan 5, 2023 · Jan 5, 2023
diff --git a/.DS_Store b/.DS_Store
diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
@@ -12,6 +12,8 @@ name: rworkflows
     - RELEASE_**
 jobs:
   rworkflows:
+    permissions:
+      contents: write
     runs-on: ${{ matrix.config.os }}
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
     container: ${{ matrix.config.cont }}
@@ -31,12 +33,6 @@ jobs:
           r: latest
           bioc: release
     steps:
-    - if: ${{ env.ACT }}
-      name: Hack container for local development
-      run: |
-        curl -fsSL https://deb.nodesource.com/setup_18.x | sudo -E bash -
-        sudo apt-get install -y nodejs
-      shell: bash {0}
     - uses: neurogenomics/rworkflows@master
       with:
         run_bioccheck: ${{ false }}
@@ -47,7 +43,7 @@ jobs:
         run_covr: ${{ true }}
         run_pkgdown: ${{ true }}
         has_runit: ${{ false }}
-        GITHUB_TOKEN: ${{ secrets.PAT_GITHUB }}
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run_docker: ${{ true }}
         docker_user: fulongyu
         docker_org: fulongyu

diff --git a/.gitignore b/.gitignore
@@ -4,3 +4,12 @@
 .Ruserdata
 Meta
 vignettes/*_cache$
+
+# find . -name .DS_Store -print0 | xargs -0 git rm -f --ignore-unmatch
+./.DS_Store
+./**/.DS_Store
+./**/**/.DS_Store
+./**/**/**/.DS_Store
+./**/**/**/**/.DS_Store
+./**/**/**/**/**/.DS_Store
+./**/**/**/**/**/**/.DS_Store
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -4,18 +4,24 @@ Version: 1.0.2
 Date: 2020-01-01
 URL: https://github.com/sankaranlab/SCAVENGE
 Authors@R: 
-    person(given = "Fulong",
+    c(person(given = "Fulong",
            family = "Yu",
            role = c("aut", "cre"),
            email = "[email protected]",
-           comment = c(ORCID = "0000-0002-6100-8300"))
+           comment = c(ORCID = "0000-0002-6100-8300")),
+    person(given = "Brian",
+           family = "Schilder",
+           role = c("ctb"),
+           email = "[email protected]",
+           comment = c(ORCID = "0000-0001-5949-2191"))
+           )
 Description: SCAVENGE (Single Cell Analysis of Variant Enrichment through 
   Network propagation of GEnomic data) optimizes the inference of functional 
   and genetic associations to specific cells at single-cell resolution.
 License: GPL (>= 2)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.2
+RoxygenNote: 7.2.3
 Depends:
     R (>= 4.0.0)
 Imports:

diff --git a/NEWS.md b/NEWS.md
@@ -14,7 +14,7 @@
 * New exported functions:
   - `example_data`
 * Add `example_results` as *data.R*
-* Add runnable example for all exported functions.
+* Add runnable examples for all exported functions.
 * Add *docker* vignette.
 
 ## Bug fixes

diff --git a/README.Rmd b/README.Rmd
@@ -1,5 +1,5 @@
 ---
-title: ""  
+title: "SCAVENGE"  
 author: "`r rworkflows::use_badges()`" 
 date: "<h4>README updated: <i>`r format( Sys.Date(), '%b-%d-%Y')`</i></h4>"
 output:
@@ -41,7 +41,6 @@ directly from GitHub by typing the following into an `R` console:
 
 ```
 if(!require("remotes")) install.packages("remotes")
-
 remotes::install_github("`r URL`")
 library(`r pkg`)
 ```
@@ -73,4 +72,4 @@ If you used or adapted SCAVENGE in your study, please cite our paper [[*Nat Biot
 
 ### Contact:
 If you run into issues and would like to report them, you can use the "Issues" tab on the left hand side.  
-Alternatively, you can contact authors: fyu{at}broadinstitute.org, lcato{at}broadinstitute.org and/or sankaran{at}broadinstitute.org.   
+Alternatively, you can contact authors: fyu{at}broadinstitute.org, lcato{at}broadinstitute.org and/or sankaran{at}broadinstitute.org.  
diff --git a/README.md b/README.md
@@ -1,18 +1,27 @@
-[![](https://img.shields.io/badge/devel%20version-1.0.2-black.svg)](https://github.com/sankaranlab/SCAVENGE)
-[![R build
-status](https://github.com/sankaranlab/SCAVENGE/workflows/rworkflows/badge.svg)](https://github.com/sankaranlab/SCAVENGE/actions)
-[![](https://img.shields.io/github/last-commit/sankaranlab/SCAVENGE.svg)](https://github.com/sankaranlab/SCAVENGE/commits/master)
-[![](https://img.shields.io/github/languages/code-size/sankaranlab/SCAVENGE.svg)](https://github.com/sankaranlab/SCAVENGE)
-[![](https://app.codecov.io/gh/sankaranlab/SCAVENGE/branch/master/graph/badge.svg)](https://app.codecov.io/gh/sankaranlab/SCAVENGE)
+SCAVENGE
+================
 [![License: GPL (\>=
 2)](https://img.shields.io/badge/license-GPL%20(%3E=%202)-blue.svg)](https://cran.r-project.org/web/licenses/GPL%20(%3E=%202))
-<!-- ¶ <h4> ¶ Authors: <i>Fulong Yu</i> ¶ </h4> -->
-### SCAVENGE: Identifying genetic trait/phenotype relevant cell type/state at single cell resolution
-<h4> ¶ Last updated: <i>Dec-01-2022</i> ¶ </h4>
+[![](https://img.shields.io/badge/devel%20version-1.0.2-black.svg)](https://github.com/sankaranlab/SCAVENGE)
+[![](https://img.shields.io/github/languages/code-size/sankaranlab/SCAVENGE.svg)](https://github.com/sankaranlab/SCAVENGE)
+[![](https://img.shields.io/github/last-commit/sankaranlab/SCAVENGE.svg)](https://github.com/sankaranlab/SCAVENGE/commits/master)
+<br> [![R build
+status](https://github.com/sankaranlab/SCAVENGE/workflows/rworkflows/badge.svg)](https://github.com/sankaranlab/SCAVENGE/actions)
+[![](https://codecov.io/gh/sankaranlab/SCAVENGE/branch/master/graph/badge.svg)](https://codecov.io/gh/sankaranlab/SCAVENGE)
+<br>
+<a href='https://app.codecov.io/gh/sankaranlab/SCAVENGE/tree/master' target='_blank'><img src='https://codecov.io/gh/sankaranlab/SCAVENGE/branch/master/graphs/icicle.svg' title='Codecov icicle graph' width='200' height='50' style='vertical-align: top;'></a>  
+<h4>  
+Authors: <i>Fulong Yu, Brian Schilder</i>  
+</h4>
+<h4>  
+README updated: <i>Mar-09-2023</i>  
+</h4>
 
+<!-- To modify Package/Title/Description/Authors fields, edit the DESCRIPTION file -->
 
+## `SCAVENGE`: Identifying genetic trait/phenotype relevant cell type/state at single cell resolution
 
-### Overview
+### Overview:
 
 Co-localization approaches using genetic variants and single-cell
 epigenomic data are unfortunately uninformative for many cells given the
@@ -54,35 +63,34 @@ We welcome you to use SCAVENGE to discover more phenotype relevant
 cells!
 
 ### Installation:
-The package
-can be installed directly from GitHub by typing the following in an
+
+Once all of the dependencies for `SCAVENGE` are installed, the package
+can be installed directly from GitHub by typing the following into an
 `R` console:
 
-```R
-if(!require("remotes")) install.packages("remotes")
+    if(!require("remotes")) install.packages("remotes")
+    remotes::install_github("https://github.com/sankaranlab/SCAVENGE")
+    library(SCAVENGE)
 
-remotes::install_github("https://github.com/sankaranlab/SCAVENGE")
-library(SCAVENGE)
-```
+## Documentation
 
-### Documentation
-
-### [Website](https://sankaranlab.github.io/SCAVENGE)
-### [Getting started](https://sankaranlab.github.io/SCAVENGE/articles/SCAVENGE)
-This web resource and vignette compiliation shows how to reproduce results of
-SCAVENGE analysis with monocyte count on a 10X PBMC dataset.
+### Tutorial:
 
-### Tutorials
+This web resource and vignette compiliation shows how to reproduce
+results of SCAVENGE analysis with monocyte count on a 10X PBMC dataset
+[\[**Vignette-pdf**\]](doc/SCAVENGE-vignette.pdf), [\[**Vignette-R
+markdown code**\]](doc/SCAVENGE-vignette.Rmd).
 
 See the [\[**Wiki
-page**\]](https://github.com/sankaranlab/SCAVENGE/wiki) for extra
-information such as preparing your GWAS data for SCAVENGE (finemapping):
-- [SCAVENGE] Preparing your GWAS data for finemapping
-- [SCAVENGE] Preparing your scATAC-seq data
-- [SCAVENGE] Rule of thumb of SCAVENGE analysis and intepretation
-- [SCAVENGE-L] SCAVENGE-L method for single cell (mt)DNA mutation-based lineage tracing analysis
+page**\]](https://github.com/sankaranlab/SCAVENGE/wiki) for some
+information on preparing your GWAS data for SCAVENGE, including
+finemapping.
+
+### [Website](https://sankaranlab.github.io/SCAVENGE)
+
+### [Getting started](https://sankaranlab.github.io/SCAVENGE/articles/SCAVENGE)
 
-### FAQs
+### FAQs:
 
 - *What input data are accepted for SCAVENGE analysis?*  
   A: The count matrix of scATAC-seq data and fine-mapped variants from
@@ -101,17 +109,18 @@ information such as preparing your GWAS data for SCAVENGE (finemapping):
   [\[**Discussions**\]](https://github.com/sankaranlab/SCAVENGE/discussions)
   page, please feel free to discuss and post your ideas.
 
-### Citation
+### Citation:
 
 If you used or adapted SCAVENGE in your study, please cite our paper
 [\[*Nat
 Biotechnol*\]](https://www.nature.com/articles/s41587-022-01341-y) \|\|
 [\[*PubMed*\]](https://pubmed.ncbi.nlm.nih.gov/35668323/).  
 *Variant to function mapping at single-cell resolution through network
-propagation.* 
-
+propagation.*
 
-### Contact
-If you run into issues and would like to report them, you can submit an [Issue](https://github.com/sankaranlab/SCAVENGE/issues).  
-Alternatively, you can contact authors: fyu{at}broadinstitute.org, lcato{at}broadinstitute.org, cweng{at}wi.mit.edu, and/or sankaran{at}broadinstitute.org.  
+### Contact:
 
+If you run into issues and would like to report them, you can use the
+“Issues” tab on the left hand side.  
+Alternatively, you can contact authors: fyu{at}broadinstitute.org,
+lcato{at}broadinstitute.org and/or sankaran{at}broadinstitute.org.
diff --git a/inst/.DS_Store b/inst/.DS_Store
diff --git a/man/.DS_Store b/man/.DS_Store
diff --git a/vignettes/.DS_Store b/vignettes/.DS_Store